Development

Setup

git clone https://github.com/CNNC-Lab/labflow.git
cd labflow
pip install -e ".[dev,docs,snakemake]"
pre-commit install  # optional

Testing

pytest                       # all tests
pytest tests/unit/ -v        # unit only
pytest tests/integration/ -v # integration
pytest --cov=labflow         # coverage

Linting

ruff check .
ruff format .

Docs

mkdocs serve   # live preview at http://localhost:8000
mkdocs build   # build static site

Adding a new resolver

1. Create src/labflow/resolvers/<name>.py subclassing EnvResolver
2. Decorate the class with @register_resolver
3. Set backend = "<name>" class attribute
4. Implement activate_command, install_command, lock_file_path, verify
5. Import it in resolvers/__init__.py
6. Add a test in tests/unit/test_resolvers.py
7. Document it under docs/guides/backends/<name>.md

Adding a new HPC system

Edit ~/.claude/contexts/hpc-systems.yaml (or the test fixture). The schema is self-documenting.

Adding a new experiment template

1. Create src/labflow/templates/<name>/run.py with an EXPERIMENT_NAME placeholder for the function name
2. Create src/labflow/templates/<name>/README.md
3. Add an entry in tests/integration/test_cli.py::test_labflow_new
4. Document under docs/concepts/experiments.md